Bulk RNA-seq ITK-SYK

Filtered data, DEG

RNA-seq

Filtering

Count matrix : This count matrix was modified like followings.
B cell genes out (Cd79a, Cd79b, Jchain)
Immunoglobulin genes out
“Ighv* ,”Igl* , “Igk*

Genes like”Igf* , “Igl* (Starting with Ig- but not Immunoglobulin genes) are not removed (checked manually)


TPM table (all genes)

PCA

PCA plot

PCA plot by condition

PCA plot version 3



Updated part from here

DEG analysis

DEG 1B vs S

  • DEG information table
  • Volcanoplot
  • Detailed information table

DEG 2B vs S

  • DEG information table

  • Volcanoplot

  • Detailed information table

Overlapping genes

From following two comparisons, significants genes(showing either up-regulation or down-regulation) were obtained.

  • DEG_1B_S
  • DEG_2B_S


Venn Diagram

Upset plot

Gene information table

Information of table

  • DEG_1BvsS : DEGs from 1B/S
  • DEG_2BvsS : DEGs from 2B/S
  • Shared : overlapping genes between 1B/S and 2B/S
DT::datatable(df, colnames = c("group", "gene"),extensions = "Buttons", options = list(dom="Bfrtip", buttons=c("csv","excel"), pageLength=10), rownames = F)

Significance of shared genes between two groups

## [1] "Significance of shared genes between two groups : p value is 0 that is significant"

GSEA

GSEA with overlapping genes’ differential expression between samples.
Overlapping genes include both up-regulated genes and down-regulated genes.

DEG 1B/S

List
1. GSEA plot colored by adjusted p value
2. GSEA plot colored by significance (FDR <= 0.05)
3. GSEA detail table





DEG 2B/S

List
1. GSEA plot colored by adjusted p value
2. GSEA plot colored by significance (FDR <= 0.05)
3. GSEA detail table.







Selected pathway analysis in 2B/S

IL6_JAK_STAT3_SIGNALING

INFLAMMATORY RESPONSE



This part is added 24.05.01

Overlapping genes (up-regulated only)


Venn Diagram

Up regualted genes

Upset plot

Up regualted genes

Gene information table

Up regualted genes

Information of table

  • DEG_1BvsS : DEGs from 1B/S
  • DEG_2BvsS : DEGs from 2B/S
  • Shared : overlapping genes between 1B/S and 2B/S

DEG UP 1B/S

List
1. GSEA plot colored by adjusted p value
2. GSEA plot colored by significance (FDR <= 0.05)
3. GSEA detail table





DEG UP 2B/S

List
1. GSEA plot colored by adjusted p value
2. GSEA plot colored by significance (FDR <= 0.05)
3. GSEA detail table.





Overlapping genes (down-regulated only)


Venn Diagram

DN regualted genes

Upset plot

DN regualted genes

Gene information table

DN regualted genes

Information of table

  • DEG_1BvsS : DEGs from 1B/S
  • DEG_2BvsS : DEGs from 2B/S
  • Shared : overlapping genes between 1B/S and 2B/S

DEG Down 1B/S

List
1. GSEA plot colored by adjusted p value
2. GSEA plot colored by significance (FDR <= 0.05)
3. GSEA detail table





DEG Down 2B/S

List
1. GSEA plot colored by adjusted p value
2. GSEA plot colored by significance (FDR <= 0.05)
3. GSEA detail table.